From 56dc5c212d7858ef8b5cffacd74831d940ce8637 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Fri, 12 Apr 2024 12:46:23 -0400 Subject: [PATCH] Revert "auto-add rgfa prefix during rgfa conversion" This reverts commit 89af9b6c89ad058234544cf8ec6468a94407d688. --- src/subcommand/convert_main.cpp | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/subcommand/convert_main.cpp b/src/subcommand/convert_main.cpp index d8981e1f02d..7474f5a521e 100644 --- a/src/subcommand/convert_main.cpp +++ b/src/subcommand/convert_main.cpp @@ -6,7 +6,6 @@ #include "../algorithms/find_gbwtgraph.hpp" #include "../io/save_handle_graph.hpp" #include "../gfa.hpp" -#include "../rgfa.hpp" #include "../gbwt_helper.hpp" #include "../gbwtgraph_helper.hpp" #include @@ -237,13 +236,6 @@ int main_convert(int argc, char** argv) { cerr << "[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead." << endl; } - // we interpret the user path selections as reference path selections (consistent with vg paths) - // so we need to add the rgfa keyword to pick up the nonref paths - if ((!rgfa_paths.empty() || !rgfa_prefixes.empty()) && - std::find(rgfa_prefixes.begin(), rgfa_prefixes.end(), RGFACover::rgfa_sample_name) == rgfa_prefixes.end()) { - rgfa_prefixes.push_back(RGFACover::rgfa_sample_name); - } - // with -F or -G we convert an alignment and not a graph if (input == input_gam || input == input_gaf) {